MANILA, Philippines – The Philippine government signed a peace accord with the country’s largest Muslim rebel group on Thursday, the culmination of years of negotiations and a significant political achievement for President Benigno Aquino III.

The deal grants largely Muslim areas of the southern Mindanao region greater political autonomy in exchange for an end to armed rebellion. But it will not stop all violence in a part of the country long plagued by lawlessness, poverty and Islamist insurgency. Implementing the ambitious accord also will be challenging.

Aquino and leaders of the Moro Islamic Liberation Front witnessed the signing of the agreement in the presidential palace in Manila. Malaysian Prime Minister Najib Razak, whose country brokered the peace talks, attended the ceremony.

“In signing this agreement, the two sides have looked not to the problems of the past, but to the promise of the future,” Najib said. “After so many years of conflict, and so many lives lost, it is a momentous act of courage.”

About 1,000 people attended the signing ceremonies, including guerrilla commanders wearing business suits instead of military uniforms who were stepping into the palace for the first time.

“For generations, fellow Filipinos in the (southern Mindanao) region were embroiled in a cycle of poverty, injustice, and violence,” Aquino said. “If we are to truly address the root causes of conflict, we must close the gap between the region and the rest of Filipino society.”

Some in the crowd wiped away tears as presidential peace adviser Teresita Deles said in a speech, her own voice breaking: “No more war! … Enough!”

The peace accord concludes formal negotiations that began in 2001. A cease-fire agreement had been in place since 1997 and has been largely observed by both sides.

More than 120,000 people have died in separatist violence since the 1970s in Mindanao, the main southern Philippine island. It is home to most of the country’s 5 million Muslims, but Christians remain the overall majority.

Previous presidents, including Corazon Aquino, Aquino’s mother, tried but failed to resolve the conflict, which has stunted growth in the region and helped foster Islamic extremism in the country and elsewhere in Southeast Asia.

Other insurgent groups in the south have vowed to keep fighting for full independence. The region is also home to the Abu Sayyaf, a Muslim extremist network with international links that the Philippine army is battling with American support.

“I will not let peace be snatched from my people again,” Aquino said. “Not now, when we have already undertaken the most difficult and most significant steps to achieve it. Those who want to test the resolve of the state will be met with a firm response based on righteousness and justice.”

Under the accord, called the Comprehensive Agreement on the Bangsamoro, the Moro Islamic Liberation Front agreed to end violence and a demand for separate state in exchange for broader autonomy. An existing five-province Muslim autonomous region is to be replaced by a more powerful, better-funded and potentially larger region to be called Bangsamoro.

Bangsamoro is the term used by the rebels to refer to Muslims as well as other ethnic groups in the southern Philippines.

Rebel chairman Murad Ibrahim lauded the “shared victory of the Bangsamoro and the Filipino people.”

He said the agreement “finally brings with it the restoration of the identity, powers and resources of the Bangsamoro. These three things which have been ours since time immemorial unjustly taken through colonization and occupation are now returned to us.”

A 15-member commission comprising rebel and government appointees is to draft a law creating the new autonomous region.

The deal calls for rebel arms to be put “beyond use” by 2016, chief government negotiator Miriam Ferrer said. The decommissioning of rebel forces and weapons has already been flagged as a potential stumbling block in a region where even politicians have private armies and guns are easy to obtain.

U.S. and EU-funded conflict resolution groups have been backing the peace process. International monitoring groups have long been in the region and will continue to support the deal for years to come.

The Catholic Bishops Conference of the Philippines welcomed the agreement and urged the government and the Moro group to reach out to those “antagonistic” toward the peace deal.

“We pray that this first courageous breakthrough will be followed by more steps leading to true and lasting peace in Mindanao,” said Archbishop Socrates Villegas, the group’s president.

The national government and the new Moro government to be formed will have to counter four other armed Muslim groups, including a breakaway faction called the Bangsamoro Islamic Freedom Fighters.

Kristian Herbolzheimer, a director of Conciliation Resources, a conflict-resolution group, said even small numbers of fighters could potentially derail the accord.

“Success will depend very much on the performance of the peace process. If they are able to deliver something to the people to show that change is coming, I think that will be major deterrent against any threat,” he said.

A 1996 accord with the then main rebel group did not end the fighting because guerrilla fighters under its chairman, Nur Misuari, continued to hold on to their weapons. Misuari’s followers and government forces clashed in September 2013 in southern Zamboanga city, killing more than 200 people.

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Associated Press writers Jim Gomez and Teresa Cerajano in Manila and Chris Brummitt in Hanoi, Vietnam, contributed to this report.